Is Drosophila-microbe association species-specific or region specific? A study undertaken involving six Indian Drosophila species

Abstract

The present work aims to identify the microbial diversity associated with six Indian Drosophila species using next generation sequencing (NGS) technology and to discover the nature of their distribution across species and eco-geographic regions. Whole fly gDNA of six Drosophila species were used to generate sequences in an Illumina platform using NGS technology. De novo based assembled raw reads were blasted against the NR database of NCBI using BLASTn for identification of their bacterial loads. We have tried to include Drosophila species from different taxonomical groups and subgroups and from three different eco-climatic regions India; four species belong to Central India, while the rest two, D. melanogaster and D. ananassae, belong to West and South India to determine both their species-wise and region-wide distribution. We detected the presence of 33 bacterial genera across all six study species, predominated by the class Proteobacteria. Amongst all, D. melanogaster was found to be the most diverse by carrying around 85% of the bacterial diversity. Our findings infer both species-specific and environment-specific nature of the bacterial species inhabiting the Drosophila host. Though the present results are consistent with most of the earlier studies, they also remain incoherent with some. The present study outcome on the host-bacteria association and their species specific adaptation may provide some insight to understand the host-microbial interactions and the phenotypic implications of microbes on the host physiology. The knowledge gained may be importantly applied into the recent insect and pest population control strategy going to implement through gut microflora in India and abroad.

The effects of taxonomy, diet, and ecology on the microbiota of riverine macroinvertebrates

“…As previously reported for a wide range of terrestrial and aquatic invertebrates (Colman et al, 2012;Jones et al, 2013;Mikaelyan et al, 2015;Muturi et al, 2017;Receveur et al, 2020;Singhal et al, 2017;Yun et al, 2014), we found significant differences in the relative abundance, alpha diversity, and beta diversity of the microbiota among host aquatic invertebrate taxa at the levels of genus, family, and order. Core microbiota, which are collections of specific bacterial species commonly shared among all individuals of a host TA B L E 4 P values from Adonis statistical tests measuring beta diversity using the unweighted and weighted UniFrac metrics and the Bray-Curtis dissimilarity metric.…”

“…A summary of the most common bacterial phyla identified within the microbiota of terrestrial invertebrates (Colman et al, 2012;Hernández-García et al, 2017;Jones et al, 2013;Mikaelyan et al, 2015;Muturi et al, 2017;Pérez-Cobas et al, 2015;Rizzi et al, 2013;Singhal et al, 2017;Yun et al, 2014) and freshwater invertebrates (Ayayee et al, 2018;Pechal & Benbow, 2016;Receveur et al, 2020), fishes (Desai et al, 2012;X. Li et al, 2013;Roeselers et al, 2011;Sullam et al, 2012;Wu et al, 2012), plants (Srivastava et al, 2017;Tanaka et al, 2012), sediments (Zhang et al, 2019), bacterioplankton (Ayayee et al, 2018;Portillo et al, 2012), and biofilms (Ayayee et al, 2018) is shown in Table 7.…”

“…Currently, microbiota studies involving invertebrates have been largely limited to terrestrial species with economic or agricultural value, such as bumble bees and honey bees, which play a vital role in crop pollination (Engel et al, 2012;Martinson et al, 2011Martinson et al, , 2012; mosquitoes, which are known vectors of viruses and pathogens (Muturi et al, 2017(Muturi et al, , 2018; and termites and red palm weevils, which are known herbivorous pests (Ayayee et al, 2015;Kitade, 2004;Mikaelyan et al, 2015;Tagliavia et al, 2014). Overall, these studies have revealed that microbiota are shaped by host taxonomy (Colman et al, 2012;Jones et al, 2013;Mikaelyan et al, 2015;Muturi et al, 2017;Singhal et al, 2017;Yun et al, 2014), environmental changes (Yun et al, 2014), and contaminants (Pennington et al, 2017), and the health of the host is often affected when these bacteria become severely disrupted, as is seen in dysbiosis (Clark & Walker, 2018;Hamdi et al, 2011;Raymann & Moran, 2018).…”

“…Currently, microbiota studies involving invertebrates have been largely limited to terrestrial species with economic or agricultural value, such as bumble bees and honey bees, which play a vital role in crop pollination (Engel et al., 2012; Martinson et al., 2011, 2012); mosquitoes, which are known vectors of viruses and pathogens (Muturi et al., 2017, 2018); and termites and red palm weevils, which are known herbivorous pests (Ayayee et al., 2015; Kitade, 2004; Mikaelyan et al., 2015; Tagliavia et al., 2014). Overall, these studies have revealed that microbiota are shaped by host taxonomy (Colman et al., 2012; Jones et al., 2013; Mikaelyan et al., 2015; Muturi et al., 2017; Singhal et al., 2017; Yun et al., 2014), environmental changes (Yun et al., 2014), and contaminants (Pennington et al., 2017), and the health of the host is often affected when these bacteria become severely disrupted, as is seen in dysbiosis (Clark & Walker, 2018; Hamdi et al., 2011; Raymann & Moran, 2018). Specifically, studies targeting host taxonomy have found that distinct bacterial taxa are exclusively limited to certain terrestrial invertebrate genera belonging to orders such as Blattodea (cockroaches and termites) (Colman et al., 2012; Kakumanu et al., 2018; Sabree et al., 2012; Sabree & Moran, 2014) and Hymenoptera (ants, bees, and wasps) (Colman et al., 2012; Koch et al, 2013; Kwong & Moran, 2015; Sauers & Sadd, 2019); measures of alpha diversity such as bacterial richness and evenness were also shown to differ significantly among eight invertebrate orders, with alpha diversity measures showing greater similarity among closely related invertebrates (Jones et al., 2013).…”

Generating high quality assemblies for genomic analysis of transposable elements

“…To illustrate this, we estimated CUSCO values for several publicly available assemblies of different D. melanogaster strains (supplementary fig. 10; (McCoy et al, 2014;Vicoso and Bachtrog, 2015;Anreiter et al, 2017;Singhal et al, 2017;Chakraborty et al, 2019;Ellison and Cao, 2020)). Assemblies based on ONT and PacBio long reads have a similar quality than our assemblies of Pi2 and Canton-S (supplementary fig.…”